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DNA-Origami-Directed Self-Assembly of Discrete Silver-Nanoparticle Architectures.

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DOI: 10.1002/ange.201000330
DNA Templates
DNA-Origami-Directed Self-Assembly of Discrete
Silver-Nanoparticle Architectures**
Suchetan Pal, Zhengtao Deng, Baoquan Ding, Hao Yan,* and Yan Liu*
2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. 2010, 122, 2760 –2764
The bottom-up organization of noble-metal nanoparticles
(NPs) with nanometer-scale precision is an important goal in
nanotechnology.[1] The DNA-guided self-assembly of these
nanoparticles has shown significant progress to meet this
challenge.[2] Enormous progress has been made in the DNAguided organization of nanoparticles into discrete,[3] onedimensional,[4] two-dimensional,[5] and three-dimensional
architectures.[6] Facile DNA-functionalization strategies for
gold nanoparticles (AuNPs) are now available, making
AuNPs preferred (easier) candidates for subsequent selfassembly to form higher-order structures. In contrast, the
mediation by DNA self-assembly of the assembly of silver
nanoparticles (AgNPs) into higher-order, well-defined discrete nanoarchitectures has not been well explored, mainly as
a result of the relative instability of these systems. Ag
undergoes oxidization more readily than Au; therefore, the
conjugated ligands on the surface of AgNPs are more labile,
and AgNPs tend to aggregate irreversibly in solutions with a
high salt concentration. However, a high salt concentration is
crucial for efficient DNA self-assembly. Recently, we and
others started to address this problem by attaching multiple
sulfur moieties to DNA[4c] to form stable AgNP–DNA
conjugates that resist aggregation in buffers with a high salt
Herein we report a bottom-up method for the fabrication
of discrete, well-ordered AgNP nanoarchitectures on selfassembled DNA origami structures of triangular shape by
using AgNPs (20 nm in diameter) conjugated with chimeric
phosphorothioated DNA (ps-po DNA) as building blocks.
Discrete monomeric, dimeric, and trimeric AgNP structures
and a AgNP–AuNP hybrid structure could be constructed
reliably in high yield. We demonstrate that the center-tocenter distance between adjacent AgNPs can be precisely
tuned from 94 to 29 nm, whereby the distance distribution is
limited by the size distribution of the nanoparticles.
DNA-origami technology[8] is a well-developed method to
create fully addressable DNA nanostructures by using
approximately 200 short staple DNA strands to fold a
single-stranded genomic DNA (e.g. the DNA of M13mp18,
7249 nucleotides long) into geometrically defined nanopatterns. In this study, we exploited the organizational power of
DNA origami to develop a robust strategy for the assembly of
otherwise hard-to-control AgNPs into well-defined nano-
architectures. As AgNPs possess unique optical properties
(for example, the local surface plasmon resonance (LSPR)
effect is stronger between AgNPs than between AuNPs), the
strategies demonstrated herein could potentially lead to
useful photonic structures enabled by the spatial control of
AgNP structures.
AgNPs (20 nm in diameter) were first functionalized with
ps-po chimeric DNA strands 9ps-T15, which had a segment of
9 bases with a phosphorothioate (9ps) backbone and a
segment of 15 regular DNA bases linked with phosphordiester bonds (T15). The nine sulfur atoms on the ps domain of
the DNA backbone provide the DNA strand with high
affinity for the surface of the AgNPs (Figure 1 a). When the
surface coverage with DNA was at saturation level, the
AgNPs showed stability against aggregation in solutions with
a high salt concentration (see the Supporting Information and
Ref. [7b] for experimental details).
Discrete AgNP architectures were then assembled in a
two-step procedure (Figure 1 b). In the first step, a triangularshaped DNA origami structure[8] was assembled with the
required number of staple strands mixed with three, six, or
nine capture strands, each with each a single-stranded overhang of approximately 15 bases that was complementary to
[*] S. Pal, Dr. Z. Deng, B. Ding, Prof. Dr. H. Yan, Prof. Dr. Y. Liu
Department of Chemistry and Biochemistry and
The Biodesign Institute, Arizona State University
Tempe, AZ 85287 (USA)
Fax: (+ 1) 480-727-2378
[**] This research was partly supported by grants from the ARO, ONR,
NSF, DOE, and NIH to Y.L. and from the ARO, ONR, NSF, DOE,
NIH, and Sloan Research Foundation to H.Y. Y.L. and H.Y. were
supported as part of the Center for Bio-Inspired Solar Fuel
Production, an Energy Frontier Research Center funded by the U.S.
Department of Energy, Office of Science, Office of Basic Energy
Sciences under Award Number DE-SC0001016.
Supporting information for this article is available on the WWW
Angew. Chem. 2010, 122, 2760 –2764
Figure 1. Schematic representation of the fabrication of discrete AgNP
architectures by DNA-origami-directed assembly. a) Functionalization
of the AgNP with ps-po chimeric DNA. b) Step 1: preparation of
preengineered triangular-shaped DNA origami displaying capture
strands at predetermined locations on the structure; step 2: hybridization of AgNPs conjugated to ps-po chimeric DNA with capture
strands on the DNA origami to form discrete dimeric AgNP architectures (I–III) with different interparticle distances as well as a trimeric
architecture (IV).
2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
the DNA strands on the AgNPs (see the Supporting
Information for DNA sequences used). However, the linkage
provided by a single hybridized segment of 15 base pairs was
not strong enough to hold a particle with a diameter of
approximately 20 nm on the origami surface (data not
shown). We therefore designed a group of three capture
strands arranged in a nearly equilateral triangle approximately 6 nm apart from one another to capture each particle
by hybridization to three complementary strands. More than
three capturing strands in each cluster, or other arrangements
of strands, may create much greater positional uncertainty.
We used A15 as the capture sequence extending from the
origami surface and T15 as the sequence on the po portion of
the chimeric DNA on the AgNP. This choice of sequence
ensures a greater degree of freedom for strand hybridization,
as it enables possible sliding[5a] of one single strand against the
other to provide enough flexibility for all three capture
strands to bind a single 20 nm AgNP simultaneously. In the
second step, preengineered DNA origami in different equivalent molar ratios was added to the DNA-functionalized
AgNPs in 1x Tris borate/EDTA buffer with 350 mm NaCl
(Tris = 2-amino-2-hydroxymethylpropane-1,3-diol, EDTA =
ethylenediaminetetraacetic acid) to form the desired structures (see the Supporting Information for experimental
details). To ensure that the reaction mixture was sufficiently
diluted to limit undesired cross-linking among the discrete
structures, we also added 1x Tris acetate/EDTA/magnesium
acetate buffer. The mixture was then annealed from 40 to 4 8C
to complete the assembly process (see the Supporting
Information for experimental details).
The formation of the triangular-shaped DNA origami
structures was first verified by transmission electron microscope imaging (TEM) of negatively stained samples (Figure 2 a). The length of each arm of the origami was
approximately 114 2 nm, which is consistent with the
designed length (Figure 1 b).
High-fidelity hybridization between capture strands and
DNA strands on the AgNPs was verified by using triangular
DNA origami that had three capture strands and was
designed to capture only one AgNP (Figure 2 b). Over 95 %
of the triangular DNA origami structures in this sample
displayed a single AgNP at one corner (see Figures S3 and S4
in the Supporting Information). Energy-dispersive X-ray
spectroscopy (EDS) of these structures showed the presence
of silver from the AgNP and uranium from the negative stain
(Figure 2 c).
To demonstrate the organizational power of our method
to create complex AgNP patterns, we further prepared
triangular-shaped DNA origami structures displaying capture
strands at unique positions to control the assembly of discrete
AgNP nanoarchitectures. Three different dimeric AgNP
structures, each with well-defined interparticle separations,
and an asymmetric trimeric AgNP structure were prepared
(Figure 1 b, I–IV and Figure 3).
Design I contains two particles at two corners of the
triangular DNA origami with a center-to-center distance of
approximately 94 nm (Figure 3, Design I). The average distance measured from TEM images of more than 100 of these
dimers was approximately 90 3 nm, which is consistent with
Figure 2. a) TEM image of the triangular DNA origami negatively
stained with uranyl formate. b) Hybridization of origami with one
AgNP. c) EDS spectrum of the sample in (b) showing the presence of
silver from the AgNP and uranium from negative staining. The Cu
detected is from the TEM grid. Scale bars on the TEM images:
100 nm.
the designed parameters. The formation of the correct dimer
AgNP structure was dominant, with a yield of about 81 %.
Since we used two equivalents of the AgNP to the origami
structure, a small population of monomeric (12.6 %) and
cross-linked structures (7.4 %) was also observed. Design II
has an interparticle center-to-center distance of approximately 52 nm by design, with a measured distance of
approximately 49 2 nm; the designed dimer structure was
formed in similarly high yield (ca. 81 %; Figure 3, Design II).
Design III has the shortest center-to-center distance of 29 nm
between the two particles by design, and a measured distance
of approximately 24 2 nm (Figure 3, Design III). TEM
images of this dimer showed a decreased yield relative to
the yields observed for the other dimer structures with larger
interparticle distances. As the AgNPs have a diameter of
approximately 20 2 nm, the measured distance of approximately 24 2 nm indicated that the edge-to-edge distance
between the particles was about 4 4 nm. It is possible that
the relatively low yield of dimers observed for design III may
2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. 2010, 122, 2760 –2764
Figure 3. Left: Illustration of individual designs I–IV with different center-to-center distances. Middle: In the first four columns are enlarged TEM
images of individual structures after negative staining of the samples with uranyl formate. The shape of the triangular DNA origami can be clearly
seen; the dark balls are the AgNPs. The fifth column shows STEM images of the samples without staining. Again, the shape of the triangular
DNA origami is clearly visible; the AgNPs appear as bright spots. Scale bars: 100 nm. Right: Yield distribution of the formed structures.
be a result of steric hindrance between the DNA strands on
the surfaces of the two approaching particles. As the diameter
of the particle is comparable to the distance between the two
groups of capture strands, another possibility is that one
particle might occupy the space between the two groups and
thus prevent the second particle from binding.
We also used a triangular-shaped origami structure with
three groups of capture strands on one arm and two different
center-to-center distances between neighboring particles: 42
and 52 nm (Figure 3, Design IV). The addition of three
equivalents of 9ps-T15-DNA-functionalized AgNPs led to
the formation of the desired assembly with an approximately
62.5 % yield of the correctly formed trimers. The middle
nanoparticle was situated asymmetrically between the other
two particles. The measured center-to-center distances of
approximately 37 2 and 45 2 nm were about 12 % shorter
than the designed distances. TEM images showed that the
three AgNPs were held on an arm of the origami triangle that
was about 10 % shorter than the other two arms. We speculate
that structural strains caused by the assembly of the three
particles on the DNA structure might have caused some
distortion of the underlining DNA structure to result in the
observed shortening of the triangle arm with the particles
For the designs shown in Figure 3, we also imaged the
structure by scanning transmission electron microscopy
(STEM; fifth column of images in Figure 3). STEM provides
a convenient way to visualize the AgNP-decorated DNA
origami samples with high contrast and without any staining.
It provided further direct evidence of the assembled structures by showing clearly the AgNPs and the underlining
triangular-shaped DNA origami nanostructures.
Angew. Chem. 2010, 122, 2760 –2764
The organization of different types of noble-metal nanoparticles with control of spatial distance and stoichiometry
remains a challenge for bottom-up nanotechnology. In this
study, we further demonstrated that DNA origami structures
can act as spatial templates for the organization of two
different types of nanoparticles through the straightforward
assembly of a stoichiometrically controlled heterodimer of an
AuNP and an AgNP (Figure 4 a). First, we selectively
modified a staple strand with a 5 nm AuNP (see the
Supporting Information and Ref. [4c] for experimental
details). The 5 nm AuNP was first attached to a specific
position on the DNA origami structure, in close proximity to
the position at which three capture strands (A15) were
designed to bind an AgNP. Second, a 9ps-T15-DNA-functionalized AgNP was added in a 1:1 ratio to fabricate the final
bimetallic discrete structure. TEM (Figure 4 b) and STEM
images (Figure 4 c) clearly showed the formation of the
designed heterodimer structure with an average center-tocenter distance of approximately 13 2 nm. EDS analysis
(Figure 4 d) during STEM imaging of the sample confirmed
the presence of both silver and gold elements. The low
abundance of Au relative to that of Ag is consistent with the
smaller size of the AuNPs.
In summary, the self-assembly of discrete AgNP and
AgNP–AuNP nanoarchitectures by using rationally designed
DNA templates enabled us to control some of the properties
that are essential for hierarchical nanoparticle assembly.
These properties include but are not limited to the spatial
relationship between the particles and the identity of the
particles. The system described herein could potentially be
used to gain better insight into particle–particle interactions.
Systematic studies with this objective are underway. Although
2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
the spatially controlled AgNP architectures, we see no
fundamental limitation now to the assembly of target
Received: January 19, 2010
Published online: March 16, 2010
Keywords: DNA origami · nanostructures · self-assembly ·
silver nanoparticles
Figure 4. a) Schematic representation of the fabrication of a dimer
structure between a 5 nm AuNP and a 20 nm AgNP. b) TEM images of
the AgNP–AuNP dimeric structure. Scale bar: 100 nm. c) STEM image
of the AgNP–AuNP dimeric structure. Scale bar: 50 nm. d) EDS
analysis of the AgNP–AuNP heterodimer on the DNA origami structure.
more systematic investigations (e.g. spectroscopic studies
combined with theoretical simulation of the assembled
structures) are needed to identify the photonic properties of
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2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. 2010, 122, 2760 –2764
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